Xiaoliang Sunney Xie

Extruding transcription elongation loops observed in high-resolution single-cell 3D genomes

The paper uses single-cell 3D genome mapping to show cohesin-mediated loop extrusion forms transcription elongation loops that enhance transcriptional burst frequency.

Single-cell Characterization of DNA Hydroxymethylation of the Mouse Brain During Aging

The paper introduces Joint-Cabernet, a single-cell platform for profiling 5hmC and 5mC, and applies it to mouse brain nuclei to study DNA hydroxymethylation changes with aging.

Quantification and potential functional relevanceof binding cooperativity of adjacent transcriptionfactors on DNA

This paper quantifies binding cooperativity between adjacent transcription factors on DNA and identifies its functional roles in gene regulation.

Mapping eukaryotic chromatin accessibility and histone modifications with DNA deaminase

The paper introduces two new methods, ChrODIE and ANDIE, for mapping chromatin accessibility and histone modifications without enzymatic cleavage, enabling multi-omics integration.

Human transcription factor combinations mapped by footprinting with deaminase

The paper introduces a method to map transcription factor binding sites genome-wide with single-base resolution and applies it to study cell-type-specific TF cooperativity in human tissues.

CGMFinder Identifies Correlated Gene Modules from 3H scRNA-seq Data

CGMFinder identifies correlated gene modules from 3H scRNA-seq data, outperforming existing methods in detecting biologically relevant modules.

Single-cell proteomics of pre-implantation mouse embryos uncovers distinct asymmetry of certain proteins among early blastomeres

The paper uses single-cell proteomics to show protein asymmetry in mouse blastomeres, independent of RNA expression, revealing a new mechanism for early cell fate determination.

Single-cell bisulfite-free 5mC and 5hmC sequencing with high sensitivity and scalability

The paper introduces Cabernet, a bisulfite-free single-cell method for high-resolution 5mC and 5hmC profiling, revealing epigenetic dynamics in mouse embryos and demonstrating scalability for complex tissues.

MINERVA: A facile strategy for SARS-CoV-2 whole genome deep sequencing of clinical samples

MINERVA enables rapid, high-quality SARS-CoV-2 whole genome sequencing from clinical samples by simplifying library preparation and improving viral enrichment.

Genomic Architecture of Cells in Tissues (GeACT): Study of Human Mid-gestation Fetus

The paper introduces GeACT, a genomic database for human mid-gestation fetus cells, linking gene expression to chromatin states and identifying key transcription factors.

Correlated Gene Modules Uncovered by Single-Cell Transcriptomics with High Detectability and Accuracy

The paper identifies correlated gene modules using single-cell RNA-seq, revealing biological functions and regulatory relationships through covariance analysis.